RATIONALE: Periodontitis is an inflammatory disease with multifactorial etiology. Vitamin D, a fat-soluble vitamin, has protective effects on inflammatory response in various systemic conditions. The clinical features of vitamin D deficiency include growth failure, hypotonia, pathologic fractures, rachitic rosary, tetany and so on. Here we present a case of 12-year-old girl affected by early-onset periodontitis accompanied with vitamin D deficiency. PATIENT CONCERNS: A 12-year-old girl with gingival redness, bleeding associated with tooth brushing, and mandibular anterior teeth movement, with difficulty in mastication for the past 2 months. There is no relevant family history or special systemic disease history. The serological microelement test showed vitamin D levels were significantly lower than normal range. Immunological test showed abnormal CD4+/CD8+(CD3+CD4+/CD3+CD8+) ratio as well. DIAGNOSES: Based on the clinical and serological findings, this patient was ultimately diagnosed with early-onset periodontitis accompanied with vitamin D deficiency. INTERVENTIONS: The main treatments for this patient were 3-fold: periodontal therapy, vitamin D supplement and oral hygiene instructions. OUTCOMES: Following 1-year therapy, periodontal conditions recovered and became stable. And serological vitamin D levels returned to normal range. LESSONS: The case of interest serves as an important reminder to clinicians, that the early-onset periodontitis may be associated with micronutrients abnormalities, and early-diagnosis and treatment could avoid the body heathy disorders.